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Yorodumi- PDB-8s0n: Crystal structure of the TMPRSS2 zymogen in complex with the nano... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8s0n | ||||||
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Title | Crystal structure of the TMPRSS2 zymogen in complex with the nanobody A07 | ||||||
Components |
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Keywords | PROTEASE/NANOBODY INHIBITOR / PROTEASE / NANOBODY / INHIBITOR / ZYMOGEN / PROTEIN BINDING / PROTEASE-NANOBODY INHIBITOR complex | ||||||
Function / homology | Function and homology information transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / Attachment and Entry / positive regulation of viral entry into host cell / serine-type endopeptidase activity / proteolysis ...transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / Attachment and Entry / positive regulation of viral entry into host cell / serine-type endopeptidase activity / proteolysis / extracellular exosome / extracellular region / nucleoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Duquerroy, S. / Fernandez, I. / Rey, F. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structural insights into TMPRSS2 maturation and HKU1 binding Authors: Fernandez, I. / Saunders, N. / Duquerroy, S. / Boland, W.H. / Arbabian, A. / Baquero, E. / Lafaye, P. / Haouz, A. / Buchrieser, J. / Schwartz, O. / Rey, F. #1: Journal: Nature / Year: 2023 Title: TMPRSS2 is a functional receptor for human coronavirus HKU1 Authors: Saunders, N. / Fernandez, I. / Planchais, C. / Michel, V. / Rajah, M.M. / Baquero Salazar, E. / Postal, J. / Porrot, F. / Guivel-Benhassine, F. / Blanc, C. / Chauveau-Le Friec, G. / Martin, ...Authors: Saunders, N. / Fernandez, I. / Planchais, C. / Michel, V. / Rajah, M.M. / Baquero Salazar, E. / Postal, J. / Porrot, F. / Guivel-Benhassine, F. / Blanc, C. / Chauveau-Le Friec, G. / Martin, A. / Grzelak, L. / Oktavia, R.M. / Meola, A. / Ahouzi, O. / Hoover-Watson, H. / Prot, M. / Delaune, D. / Cornelissen, M. / Deijs, M. / Meriaux, V. / Mouquet, H. / Simon-Loriere, E. / van der Hoek, L. / Lafaye, P. / Rey, F. / Buchrieser, J. / Schwartz, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8s0n.cif.gz | 444 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8s0n.ent.gz | 303.3 KB | Display | PDB format |
PDBx/mmJSON format | 8s0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8s0n_validation.pdf.gz | 463.1 KB | Display | wwPDB validaton report |
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Full document | 8s0n_full_validation.pdf.gz | 475.1 KB | Display | |
Data in XML | 8s0n_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 8s0n_validation.cif.gz | 47.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/8s0n ftp://data.pdbj.org/pub/pdb/validation_reports/s0/8s0n | HTTPS FTP |
-Related structure data
Related structure data | 8s0lC 8s0mC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 43922.445 Da / Num. of mol.: 2 / Mutation: S441A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Production host: Drosophila melanogaster (fruit fly) References: UniProt: O15393, transmembrane protease serine 2 #2: Antibody | Mass: 16031.511 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10 %w/v PEG 3000, 0.1 M imidazole (pH 8.0), 0.2 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2023 |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978565 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 50880 / % possible obs: 95 % / Redundancy: 7 % / Biso Wilson estimate: 40.89 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.097 / Rrim(I) all: 0.259 / Net I/av σ(I): 6.598 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.3→2.39 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.236 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2545 / CC1/2: 0.316 / Rpim(I) all: 0.912 / Rrim(I) all: 2.417 / % possible all: 39.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.42 Å / SU ML: 0.332 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.9624 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→24.42 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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